Prevent Blender to add numbers behind materials when importing a FBX
Hopefully, using a Material Specials addon could do the job for you:


Enable it in User Preferences (CtrlAltU) > Addons.


After you import your model, use the slots menu by clicking the arrow down button (beside material slots list) and navigate to Specials > Merge Base Names


Set AutoRename and click OK, it should remove .00X from all materials (not only for selected object)



If you get multiple materials with the same name, you can try Clean Material Slots function: